Abstract: To  evaluate the choice preference of fish habitat in the Yangtze estuary, juvenile Collichthys lucidus which is the dominant species in spring was selected. The 4 indicator factors, including abundance of Pseudograpsus albus, salinity, substrate type and water depth, were selected from 19 environmental factors. Then, the indices of the habitat suitability curves of the 4 indicator factors were established, and the HSI of juvenile C. lucidus at each site was calculated. The results indicated that HSI was almost more than 0.5 in North Branch, and less than 0.2 in South Branch. It showed that the North Branch of Yangtze estuary was the main nursery area of C. lucidus. The most suitable growth sector was the area with salinity more than 14, mean grain size of substrate less than 29 μm and water depth 2 to 5 m, which was consistent with the distribution of HSI. The study demonstrated that biological factors could be characterized by the response of juvenile C. lucidus to the environment. Chemical oxygen demand, ammonium nitrogen, total phosphorus and volatile phenol did not have significant correlation with the fish abundance, with which nitrite nitrogen, nitrate nitrogen and total nitrogen had significant positive correlation. It suggested that the eutrophication of the survey area had not damaged the habitat of C. lucidus. However, copper ion and cadmium ion had significant negative correlation with the fish abundance, which indicated that the heavy metal pollution had harmed the growth and distribution of juvenile C. lucidus. It was inferred that the heavy metal pollution was the restrictive factor influencing the fish habitat in Yangtze estuary.